When using the STRIP option for paragraph behaviors, paragraph markers following headers and references (\s1, \r, \rem) are stripped, except for beginning-of-chapter headers/references (i.e. in verse 0 of a given chapter). I believe this is expected behavior, but I don't think it creates valid USFM, or at least not the USFM we want. Because header and reference markers are themselves paragraph markers, any text between them and the next paragraph marker will go in that header/reference, even if a new verse starts.
So, I think we always need to keep the paragraph marker that immediately follows a header or reference (or a block of them, consecutive \s1 \r is common).